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1FYT
Biol. Unit 1
Info
Asym.Unit (142 KB)
Biol.Unit 1 (136 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELL RECEPTOR, INFLUENZA HA ANTIGEN PEPTIDE, AND MHC CLASS II MOLECULE, HLA-DR1
Authors
:
J. Hennecke, A. Carfi, D. C. Wiley
Date
:
03 Oct 00 (Deposition) - 08 Nov 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Protein-Protein Complex, Immunoglobulin Fold, Immune System
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
J. Hennecke, A. Carfi, D. C. Wiley
Structure Of A Covalently Stabilized Complex Of A Human Alphabeta T-Cell Receptor, Influenza Ha Peptide And Mhc Class Ii Molecule, Hla-Dr1.
Embo J. V. 19 5611 2000
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:76 , SER A:77 , ASN A:78
BINDING SITE FOR RESIDUE NAG A 501
2
AC2
SOFTWARE
ASN A:118 , GLU A:166 , TRP A:168
BINDING SITE FOR RESIDUE NAG A 511
[
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SAPs(SNPs)/Variants
(25, 25)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_033379 (R4K, chain B, )
02: VAR_033380 (R4Q, chain B, )
03: VAR_016740 (Q10E, chain B, )
04: VAR_033381 (S37Y, chain B, )
05: VAR_016741 (G45R, chain B, )
06: VAR_033382 (Y47F, chain B, )
07: VAR_033383 (Y60S, chain B, )
08: VAR_016710 (L67I, chain B, )
09: VAR_016711 (Q70D, chain B, )
10: VAR_033384 (Q70E, chain B, )
11: VAR_033385 (Q70H, chain B, )
12: VAR_016742 (R71A, chain B, )
13: VAR_016712 (R71E, chain B, )
14: VAR_033386 (A73G, chain B, )
15: VAR_033387 (A74E, chain B, )
16: VAR_016713 (T77N, chain B, )
17: VAR_033388 (Y78H, chain B, )
18: VAR_016714 (V85A, chain B, )
19: VAR_016715 (G86V, chain B, )
20: VAR_033389 (G135D, chain B, )
21: VAR_033390 (A140T, chain B, )
22: VAR_033391 (V142M, chain B, )
23: VAR_033392 (Q149H, chain B, )
24: VAR_033393 (R166Q, chain B, )
25: VAR_033394 (T181I, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_033379
R
33
K
2B11_HUMAN
Polymorphism
34716432
B
R
4
K
02
UniProt
VAR_033380
R
33
Q
2B11_HUMAN
Polymorphism
34716432
B
R
4
Q
03
UniProt
VAR_016740
Q
39
E
2B11_HUMAN
Polymorphism
---
B
Q
10
E
04
UniProt
VAR_033381
S
66
Y
2B11_HUMAN
Polymorphism
16822820
B
S
37
Y
05
UniProt
VAR_016741
G
74
R
2B11_HUMAN
Polymorphism
---
B
G
45
R
06
UniProt
VAR_033382
Y
76
F
2B11_HUMAN
Polymorphism
1060346
B
Y
47
F
07
UniProt
VAR_033383
Y
89
S
2B11_HUMAN
Polymorphism
36074728
B
Y
60
S
08
UniProt
VAR_016710
L
96
I
2B11_HUMAN
Polymorphism
---
B
L
67
I
09
UniProt
VAR_016711
Q
99
D
2B11_HUMAN
Polymorphism
---
B
Q
70
D
10
UniProt
VAR_033384
Q
99
E
2B11_HUMAN
Polymorphism
17881965
B
Q
70
E
11
UniProt
VAR_033385
Q
99
H
2B11_HUMAN
Polymorphism
17879599
B
Q
70
H
12
UniProt
VAR_016742
R
100
A
2B11_HUMAN
Polymorphism
---
B
R
71
A
13
UniProt
VAR_016712
R
100
E
2B11_HUMAN
Polymorphism
---
B
R
71
E
14
UniProt
VAR_033386
A
102
G
2B11_HUMAN
Polymorphism
17878857
B
A
73
G
15
UniProt
VAR_033387
A
103
E
2B11_HUMAN
Polymorphism
16822805
B
A
74
E
16
UniProt
VAR_016713
T
106
N
2B11_HUMAN
Polymorphism
16822752
B
T
77
N
17
UniProt
VAR_033388
Y
107
H
2B11_HUMAN
Polymorphism
16822512
B
Y
78
H
18
UniProt
VAR_016714
V
114
A
2B11_HUMAN
Polymorphism
17424145
B
V
85
A
19
UniProt
VAR_016715
G
115
V
2B11_HUMAN
Polymorphism
2230810
B
G
86
V
20
UniProt
VAR_033389
G
164
D
2B11_HUMAN
Polymorphism
1059633
B
G
135
D
21
UniProt
VAR_033390
A
169
T
2B11_HUMAN
Polymorphism
2308768
B
A
140
T
22
UniProt
VAR_033391
V
171
M
2B11_HUMAN
Polymorphism
701829
B
V
142
M
23
UniProt
VAR_033392
Q
178
H
2B11_HUMAN
Polymorphism
701830
B
Q
149
H
24
UniProt
VAR_033393
R
195
Q
2B11_HUMAN
Polymorphism
3205588
B
R
166
Q
25
UniProt
VAR_033394
T
210
I
2B11_HUMAN
Polymorphism
17423930
B
T
181
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:161-167)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
DRA_HUMAN
186-192
1
A:161-167
2B11_HUMAN
200-206
1
B:171-177
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(8, 8)
Info
All SCOP Domains
1a: SCOP_d1fyta1 (A:82-181)
2a: SCOP_d1fytb1 (B:93-190)
3a: SCOP_d1fytd2 (D:118-203)
4a: SCOP_d1fyte2 (E:119-246)
5a: SCOP_d1fytd1 (D:1-117)
6a: SCOP_d1fyte1 (E:3-118)
7a: SCOP_d1fyta2 (A:2-81)
8a: SCOP_d1fytb2 (B:3-92)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
Class II MHC alpha chain, C-terminal domain
(75)
Human (Homo sapiens), HLA-DR group [TaxId: 9606]
(37)
1a
d1fyta1
A:82-181
Protein domain
:
Class II MHC beta chain, C-terminal domain
(70)
Human (Homo sapiens), HLA-DR group [TaxId: 9606]
(40)
2a
d1fytb1
B:93-190
Protein domain
:
T-cell antigen receptor
(81)
Human (Homo sapiens), alpha-chain [TaxId: 9606]
(20)
3a
d1fytd2
D:118-203
Human (Homo sapiens), beta-chain [TaxId: 9606]
(29)
4a
d1fyte2
E:119-246
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
T-cell antigen receptor
(105)
Human (Homo sapiens), alpha-chain [TaxId: 9606]
(21)
5a
d1fytd1
D:1-117
Human (Homo sapiens), beta-chain [TaxId: 9606]
(29)
6a
d1fyte1
E:3-118
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
Class II MHC alpha chain, N-terminal domain
(75)
Human (Homo sapiens), HLA-DR1 [TaxId: 9606]
(18)
7a
d1fyta2
A:2-81
Protein domain
:
Class II MHC beta chain, N-terminal domain
(70)
Human (Homo sapiens), HLA-DR1 [TaxId: 9606]
(17)
8a
d1fytb2
B:3-92
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1fytB01 (B:3-92)
1b: CATH_1fytA01 (A:3-81)
2a: CATH_1fytE01 (E:3-118)
2b: CATH_1fytD02 (D:117-202)
2c: CATH_1fytA02 (A:82-181)
2d: CATH_1fytE02 (E:119-246)
2e: CATH_1fytB02 (B:93-190)
2f: CATH_1fytD01 (D:1-116)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
(75)
Homologous Superfamily
:
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
(75)
Human (Homo sapiens)
(48)
1a
1fytB01
B:3-92
1b
1fytA01
A:3-81
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1fytE01
E:3-118
2b
1fytD02
D:117-202
2c
1fytA02
A:82-181
2d
1fytE02
E:119-246
2e
1fytB02
B:93-190
2f
1fytD01
D:1-116
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Hetero
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Protein & NOT Variant
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Protein & NOT PROSITE
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Chain E
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Asym.Unit (142 KB)
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